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read dim variable of sparse dset to compress storage of indices in HDF5
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@ -2445,6 +2445,10 @@ trexio_read_$group_dset$(trexio_t* const file,
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rc = trexio_read_$group_dset$_size(file, &size_max);
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rc = trexio_read_$group_dset$_size(file, &size_max);
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if (rc != TREXIO_SUCCESS) return rc;
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if (rc != TREXIO_SUCCESS) return rc;
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int64_t num;
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rc = trexio_read_$group_dset_sparse_dim$_64(file, &num);
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if (rc != TREXIO_SUCCESS) return rc;
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// introduce a new variable which will be modified with the number of integrals being read if EOF is encountered
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// introduce a new variable which will be modified with the number of integrals being read if EOF is encountered
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uint64_t eof_read_size = 0UL;
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uint64_t eof_read_size = 0UL;
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@ -2456,7 +2460,7 @@ trexio_read_$group_dset$(trexio_t* const file,
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case TREXIO_HDF5:
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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#ifdef HAVE_HDF5
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rc = trexio_hdf5_read_$group_dset$(file, offset_file, buffer_size, size_max, &eof_read_size, index_sparse, value_sparse);
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rc = trexio_hdf5_read_$group_dset$(file, offset_file, buffer_size, num, &eof_read_size, index_sparse, value_sparse);
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break;
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break;
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#else
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#else
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rc = TREXIO_BACK_END_MISSING;
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rc = TREXIO_BACK_END_MISSING;
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@ -2543,6 +2547,10 @@ trexio_write_$group_dset$(trexio_t* const file,
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if (rc != TREXIO_SUCCESS && rc != TREXIO_DSET_MISSING) return rc;
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if (rc != TREXIO_SUCCESS && rc != TREXIO_DSET_MISSING) return rc;
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if (rc == TREXIO_DSET_MISSING) size_max = 0L;
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if (rc == TREXIO_DSET_MISSING) size_max = 0L;
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int64_t num;
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rc = trexio_read_$group_dset_sparse_dim$_64(file, &num);
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if (rc != TREXIO_SUCCESS) return rc;
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int32_t* index_sparse_p = (int32_t*) index_sparse;
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int32_t* index_sparse_p = (int32_t*) index_sparse;
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// shift indices to be zero-based if Fortran API is used
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// shift indices to be zero-based if Fortran API is used
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if (file->one_based) {
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if (file->one_based) {
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@ -2565,7 +2573,7 @@ trexio_write_$group_dset$(trexio_t* const file,
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case TREXIO_HDF5:
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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#ifdef HAVE_HDF5
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rc = trexio_hdf5_write_$group_dset$(file, offset_file, buffer_size, size_max, index_sparse_p, value_sparse);
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rc = trexio_hdf5_write_$group_dset$(file, offset_file, buffer_size, num, index_sparse_p, value_sparse);
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break;
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break;
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#else
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#else
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rc = TREXIO_BACK_END_MISSING;
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rc = TREXIO_BACK_END_MISSING;
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@ -107,7 +107,7 @@ def recursive_populate_file(fname: str, paths: dict, detailed_source: dict) -> N
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'group_num_f_dtype_default', 'group_num_f_dtype_double', 'group_num_f_dtype_single',
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'group_num_f_dtype_default', 'group_num_f_dtype_double', 'group_num_f_dtype_single',
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'group_num_dtype_default', 'group_num_dtype_double', 'group_num_dtype_single',
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'group_num_dtype_default', 'group_num_dtype_double', 'group_num_dtype_single',
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'group_num_h5_dtype', 'group_num_py_dtype',
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'group_num_h5_dtype', 'group_num_py_dtype',
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'group_dset_format_scanf', 'group_dset_format_printf',
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'group_dset_format_scanf', 'group_dset_format_printf', 'group_dset_sparse_dim',
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'group_dset_sparse_line_length', 'group_dset_sparse_indices_printf', 'group_dset_sparse_indices_scanf',
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'group_dset_sparse_line_length', 'group_dset_sparse_indices_printf', 'group_dset_sparse_indices_scanf',
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'group_dset', 'group_num', 'group_str', 'group']
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'group_dset', 'group_num', 'group_str', 'group']
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@ -707,6 +707,8 @@ def split_dset_dict_detailed (datasets: dict) -> tuple:
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tmp_dict['group_dset_f_dims'] = dim_f_list
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tmp_dict['group_dset_f_dims'] = dim_f_list
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if is_sparse:
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if is_sparse:
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# store the max possible dim of the sparse dset (e.g. mo_num)
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tmp_dict['group_dset_sparse_dim'] = tmp_dict['dims'][0]
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# build printf/scanf sequence and compute line length for n-index sparse quantity
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# build printf/scanf sequence and compute line length for n-index sparse quantity
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index_printf = f'*(index_sparse + {str(rank)}*i'
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index_printf = f'*(index_sparse + {str(rank)}*i'
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index_scanf = f'index_sparse + {str(rank)}*i'
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index_scanf = f'index_sparse + {str(rank)}*i'
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